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Sample GSM768764 Query DataSets for GSM768764
Status Public on Jun 30, 2012
Title Control 2
Sample type RNA
 
Source name Peripheral Blood, control 2
Organism Homo sapiens
Characteristics tissue: Peripheral blood
cell type: non-specific immunoisolated cells
Extracted molecule total RNA
Extraction protocol Circulating Tumor Cells (CTC) were immunoisolated from 7.5ml of peripheral blood from six metastatic colorectal patients. Blood was also obtained from three healthy donors. After immunoisolation, RNA was purified with the Qiamp Viral Mini kit (Qiagen) and globally amplified with a whole transcriptome amplification system (WTA2, Sigma-Aldrich). Final cDNA was purified by using the Qiaquick system (Qiagen).
Label Cy3
Label protocol 1.65 µg of cDNA was ULS-Cy3 labeled following manufacturer instructions. Samples were incubated at 85ºC for 30 minutes. After removing non-reacted ULS, labeling degrees were evaluated as recommended. For detailed methods see Agilent G4112-90000 protocol.
 
Hybridization protocol Labeled cDNA was mixed with the Agilent hybridization master mix, incubated at 95ºC for 3 minutes. Afterwards, samples were dispensed onto 4x44K microarrays. For detailed methods see Agilent G4112-90000 protocol.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um).
Description Gene expression of non-specific immunoisolated cells
Data processing The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95 and Grid:016528_D_F_20070525) to obtain Processed Signal intensities. The following features and/or genes which did not conform to the established quality criteria were filtered: i) non-uniform pixel distributed outliers and population replicate outliers according to the default Agilent feature extraction criteria; ii) features whose ratio between processed signal and its error was below 2; iii) spots not differentiated from background signal (as estimated for each spot). Normalization was done with the quantile method implemented in the Limma Bioconductor package.
 
Submission date Jul 28, 2011
Last update date Jun 30, 2012
Contact name Miguel Abal
E-mail(s) miguel.abal.posada@sergas.es
Phone 0034981955073
Organization name University Clinical Hospital
Department Medical Oncology
Lab Translational Oncology Laboratory
Street address Trav Choupana s/n
City Santiago de Compostela
State/province A Coruña
ZIP/Postal code 15706
Country Spain
 
Platform ID GPL13497
Series (1)
GSE31023 Molecular characterisation of circulating tumor cells in human metastatic colorectal cancer

Data table header descriptions
ID_REF
VALUE filtered gprocessed signal intensities

Data table
ID_REF VALUE
A_23_P100001 609
A_23_P100022 241
A_23_P100056
A_23_P100074 243
A_23_P100127 247
A_23_P100141 619
A_23_P100189 1614
A_23_P100196 2033
A_23_P100203
A_23_P100220 3532
A_23_P100240 286
A_23_P10025 194
A_23_P100292 931
A_23_P100315
A_23_P100326 233
A_23_P100344
A_23_P100355 3383
A_23_P100386 188
A_23_P100392 587
A_23_P100420

Total number of rows: 34183

Table truncated, full table size 554 Kbytes.




Supplementary file Size Download File type/resource
GSM768764.txt.gz 9.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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